Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_106719566.1 CU100_RS26145 amidase
Query= curated2:A1ATL3 (485 letters) >NCBI__GCF_003010935.1:WP_106719566.1 Length = 488 Score = 199 bits (505), Expect = 2e-55 Identities = 150/489 (30%), Positives = 227/489 (46%), Gaps = 38/489 (7%) Query: 2 DLFDLTLHELHAKLKSKEVSSREATSAMLDRIAELEPRINAFITVTPERALAEAEAADR- 60 DL L + L + ++S+ E T A L RIA+ + ++NA++ V + A A + D Sbjct: 10 DLCFLPVSRLSEMRATGKISTAEITEAYLSRIAKFDSKLNAYVEVYAKEARLAATSLDAG 69 Query: 61 RIAAGEADVLTGIPLAVKDIFLTEGTLTTCGSRILNNFIPPYSATSFEKLKQRGMVLLGK 120 R + + GIP+A+KD+ +G +TT GS +A+ +L G ++LGK Sbjct: 70 RDTRNDGGLACGIPIALKDLLEVDGKITTAGSAHFRGRRSCVTASLARRLISSGSIILGK 129 Query: 121 LNQDEFAMGSSNESSASGPCRNPWNTDC--IPGGSSGGSAAAIAARQATVTLGTDTGGSI 178 EFA + G NPW+ D IPGGSS GSA A++ A +GTDTGGS+ Sbjct: 130 TQTVEFAYSGWGINPQMGTPWNPWDEDIQRIPGGSSSGSAVAVSGSLAPWAIGTDTGGSV 189 Query: 179 RQPASHCGCVGLKPTYGRVSRYGVIAYASSLDQVGPLTRDVTDCAIMLGALAGHDPKDST 238 R PAS CG LK T +++ G+I + + D GP+TR V D AI+ + G + + + Sbjct: 190 RLPASFCGVTALKTTADQIATDGIIPLSKTFDTPGPITRSVLDAAILYNVMLGSESQFAF 249 Query: 239 SVDRPVPDYQAALTNDIRGLRIGLPREYFIEGLDPDVQASMDQAIETYRRLGAEFTEISL 298 V AL + GL++G + EG++ DV + D+++ET LGAE E +L Sbjct: 250 G-SGTVIGISRALEGGVLGLKLGSLPKAEREGVEADVLEAYDRSLETLSNLGAEIVETNL 308 Query: 299 P-HTDYAVASYYLIATAEASANLARYDGVRFGHRAEQAEGLLEMYSRSRSQGFGSEVKRR 357 P + I +EA A F + LL+ V+ Sbjct: 309 PFRFQDCFGPHMSIVNSEAYA--------YFRDVIDDGSSLLD-----------ESVREG 349 Query: 358 IMLGTYALSSGYYDAYYLKAQKVRTLIMADFIQAFEGVDLILTPVAPTPAFRIG--EKVN 415 I G Y DA+ + + A A VD +LTP + A + ++ Sbjct: 350 ISAGRTISPQQYSDAF-----EQISRFKAQISGALVNVDALLTPTTLSVALPVEGLDRSR 404 Query: 416 DPLQMYLSDIFTIPVNLAGTCAMSLPAGISGQGLPIGVQLIGKPFGEETILRAAHAFEQA 475 P + FT VN G C ++LP G + + LP +Q++ + E LR AF+QA Sbjct: 405 PPSR------FTRFVNTLGMCGLALPNGKNAEDLPTSLQIVCREHQERLALRIGLAFQQA 458 Query: 476 TEWHSLRAP 484 T WH LR P Sbjct: 459 TSWH-LRRP 466 Lambda K H 0.318 0.134 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 496 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 485 Length of database: 488 Length adjustment: 34 Effective length of query: 451 Effective length of database: 454 Effective search space: 204754 Effective search space used: 204754 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory